             [clojure.java.io :as io])
   (:import match.Match2))
 
-(declare region-query-s)
-(declare region-query-p)
-(declare memoized-metric)
-
-;; TODO: find optimal subdivision for r/fold
-
-(def memoized-dbscan
-  "If true, calls to the metric passed to dbscan will be memoized"
-  true)
-
-(def memoized-mediods
-  "If true, calls to the metric passed to mediod-protein will be memoized"
-  true)
-
-(def region-query
-  "Select region-query-s (serial) or region-query-p (parallel)"
-  region-query-p)
-
-(def partition-size
-  "Approximate subdivision size for clojure.core.reducers/fold"
-  16)
-
-;;;
+(declare memoize-metric)
+(declare partition-size)
+(declare region-query)
+(declare memoized-dbscan)
+(declare memoized-medioids)
+
 
 (defn region-query-s
   "Serial region query; returns all pts *at least* eps similar to pt."

    (for [rep cluster-reps]
      [(metric pt rep), rep])))

;;;

(def files
  ["UniRef90_A0A060TYH3.fa", "UniRef90_I0C6W8.fa","UniRef90_Q0A457.fa",

  (reduce into 
          (map read-fasta (take 10 prefixed-files))))

(time (def trial (dbscan sample-proteins protein-metric 100 4)))


;;; Test code (I know, I know, I should have written a real test suite.)

(comment

